近日，浙江大学方磊等研究人员合作发现，207个棉花品种在单核苷酸分辨率下的群体范围内DNA甲基化多态性，揭示了表观基因组对复杂性状的贡献。2024年10月17日，《细胞研究》杂志在线发表了这项成果。

研究人员调查了来自207个品种的开花20天后（DPA）棉花纤维的高质量甲基组、转录组和基因组，并将经典的群体遗传学框架扩展到表观遗传学。研究人员鉴定了超过2.87亿个单甲基化多态性（SMP），这是单核苷酸多态性（SNP）数量的100倍。这些SMP在基因内区域显著富集，而在可转座元件中减少。关联分析进一步识别了总计5426782个顺式甲基化数量性状基因位点（cis-meQTL）、5078个顺式表达数量性状甲基化（cis-eQTM）和9157个表达数量性状基因位点（eQTL）。

值得注意的是，36.39%的cis-eQTM基因与遗传变异无关，这表明与基因表达变异相关的大量SMP独立于SNP。此外，在与产量和纤维质量性状相关的1715个表观遗传位点中，仅有36个（2.10%）与全基因组关联研究（GWAS）位点共享。多组学调控网络的构建揭示了43个可能参与纤维发育的cis-eQTM基因，这些基因无法仅通过GWAS识别。在这些基因中，一个编码CBL相互作用蛋白激酶10的基因在纤维长度调控中的作用通过基因编辑得到了成功验证。

综合来看，这些发现证明DNA甲基化数据可以作为育种的额外资源，并为提升和加速作物改良过程提供机会。

据了解，DNA甲基化在作物发育中发挥多重调控作用。然而，甲基化多态性与遗传多态性、基因表达和自然作物种群表型变异之间的关系仍然大量未知。

附：英文原文

Title: Population-wide DNA methylation polymorphisms at single-nucleotide resolution in 207 cotton accessions reveal epigenomic contributions to complex traits

Author: Zhao, Ting, Guan, Xueying, Hu, Yan, Zhang, Ziqian, Yang, Han, Shi, Xiaowen, Han, Jin, Mei, Huan, Wang, Luyao, Shao, Lei, Wu, Hongyu, Chen, Qianqian, Zhao, Yongyan, Pan, Jiaying, Hao, Yupeng, Dong, Zeyu, Long, Xuan, Deng, Qian, Zhao, Shengjun, Zhang, Mengke, Zhu, Yumeng, Ma, Xiaowei, Chen, Zequan, Deng, Yayuan, Si, Zhanfeng, Li, Xin, Zhang, Tianzhen, Gu, Fei, Gu, Xiaofeng, Fang, Lei

Issue&Volume: 2024-10-17

Abstract: DNA methylation plays multiple regulatory roles in crop development. However, the relationships of methylation polymorphisms with genetic polymorphisms, gene expression, and phenotypic variation in natural crop populations remain largely unknown. Here, we surveyed high-quality methylomes, transcriptomes, and genomes obtained from the 20-days-post-anthesis (DPA) cotton fibers of 207 accessions and extended the classical framework of population genetics to epigenetics. Over 287 million single methylation polymorphisms (SMPs) were identified, 100 times more than the number of single nucleotide polymorphisms (SNPs). These SMPs were significantly enriched in intragenic regions while depleted in transposable elements. Association analysis further identified a total of 5,426,782 cis-methylation quantitative trait loci (cis-meQTLs), 5078 cis-expression quantitative trait methylation (cis-eQTMs), and 9157 expression quantitative trait loci (eQTLs). Notably, 36.39% of cis-eQTM genes were not associated with genetic variation, indicating that a large number of SMPs associated with gene expression variation are independent of SNPs. In addition, out of the 1715 epigenetic loci associated with yield and fiber quality traits, only 36 (2.10%) were shared with genome-wide association study (GWAS) loci. The construction of multi-omics regulatory networks revealed 43 cis-eQTM genes potentially involved in fiber development, which cannot be identified by GWAS alone. Among these genes, the role of one encoding CBL-interacting protein kinase 10 in fiber length regulation was successfully validated through gene editing. Taken together, our findings prove that DNA methylation data can serve as an additional resource for breeding purposes and can offer opportunities to enhance and expedite the crop improvement process.

DOI: 10.1038/s41422-024-01027-x

Source: https://www.nature.com/articles/s41422-024-01027-x